Hervé Pagès
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/GenomicRanges |
| git_branch: RELEASE_3_21 |
| git_last_commit: 9d5d73b |
| git_last_commit_date: 2025-04-15 09:46:56 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 844/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicRanges 1.60.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the GenomicRanges package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicRanges.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: GenomicRanges |
| Version: 1.60.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GenomicRanges |
| StartedAt: 2025-10-15 15:14:02 -0400 (Wed, 15 Oct 2025) |
| EndedAt: 2025-10-15 15:14:23 -0400 (Wed, 15 Oct 2025) |
| EllapsedTime: 21.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GenomicRanges
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘GenomicRanges’ ...
** this is package ‘GenomicRanges’ version ‘1.60.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c transcript_utils.c -o transcript_utils.o
In function ‘tloc2rloc’,
inlined from ‘tlocs2rlocs’ at transcript_utils.c:208:26:
transcript_utils.c:143:45: warning: ‘start’ may be used uninitialized [-Wmaybe-uninitialized]
143 | return on_minus_strand ? end - tloc : start + tloc;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c: In function ‘tlocs2rlocs’:
transcript_utils.c:120:24: note: ‘start’ was declared here
120 | int nexons, j, start, end, width;
| ^~~~~
In function ‘tloc2rloc’,
inlined from ‘tlocs2rlocs’ at transcript_utils.c:208:26:
transcript_utils.c:143:45: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized]
143 | return on_minus_strand ? end - tloc : start + tloc;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c: In function ‘tlocs2rlocs’:
transcript_utils.c:120:31: note: ‘end’ was declared here
120 | int nexons, j, start, end, width;
| ^~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-GenomicRanges/00new/GenomicRanges/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicRanges)